.\" generated with Ronn/v0.7.3
.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.TH "SAMBAMBA\-FLAGSTAT" "1" "August 2014" "" ""
.
.SH "NAME"
\fBsambamba\-flagstat\fR \- getting flag statistics from BAM file
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.SH "SYNOPSIS"
\fBsambamba flagstat\fR \fIOPTIONS\fR <input\.bam>
.
.SH "DESCRIPTION"
Outputs some statistics drawn from read flags\.
.
.P
First line contains numbers of QC\-passed and QC\-failed reads\. Then come pairs of numbers, the former for QC\-passed reads, the latter for QC\-failed ones:
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.IP "\(bu" 4
duplicates
.
.IP "\(bu" 4
mapped reads (plus percentage relative to the numbers from the first line)
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.IP "\(bu" 4
reads with \'is_paired\' flag set
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.IP "\(bu" 4
paired reads which are first mates
.
.IP "\(bu" 4
paired reads which are second mates
.
.IP "\(bu" 4
paired reads with \'proper_pair\' flag set (plus percentage relative to the numbers of QC\-passed/failed reads with \'is_paired\' flag set)
.
.IP "\(bu" 4
paired reads where both mates are mapped
.
.IP "\(bu" 4
paired reads where read itself is unmapped but mate is mapped
.
.IP "\(bu" 4
paired reads where mate is mapped to a different chromosome
.
.IP "\(bu" 4
the same as previous but mapping quality is not less than 5
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.IP "" 0
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.SH "OPTIONS"
.
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fINTHREADS\fR
Specify number of threads to use for BAM decompression
.
.TP
\fB\-p\fR, \fB\-\-show\-progress\fR
Show progressbar in STDERR

